log passes

bin/identify_tophit_and_contaminants2.py

@@ -483,6 +483,7 @@ def process_reports(afanc_json_path, kraken_json_path, supposed_species, unmix_m
     parser.add_argument('myco_dir', metavar='myco_dir', type=str, help='Path to myco directory')
     parser.add_argument('prev_species_json', metavar='prev_species_json', type=str, help='Path to previous species json file. Can be set to \'null\'')
     parser.add_argument('permissive', metavar='permissive', type=str, help="Is either \'yes\' or \'no\', given in response to the question: do you want to carry on to Clockwork regardless of errors?")
+    parser.add_argument('pass_number', metavar='pass_number', type=int, help="Pass number. Refers to what pass of decontamination the pipeline is on")
     args = parser.parse_args()
 
     # REQUIREMENTS
@@ -495,6 +496,7 @@ def process_reports(afanc_json_path, kraken_json_path, supposed_species, unmix_m
     myco_dir = sys.argv[6]
     prev_species_json = sys.argv[7]
     permissive = sys.argv[8]
+    pass_number = sys.argv[9]
 
     # read assembly summary
     urls, tax_ids = read_assembly_summary(assembly_file)
@@ -509,6 +511,6 @@ def process_reports(afanc_json_path, kraken_json_path, supposed_species, unmix_m
             f.write(url + "\n")
 
     # print final file
-    out_file2 = sample_id + '_species_in_sample.json'
+    out_file2 = sample_id + '_species_in_sample_pass_' + str(pass_number) + '.json'
     with open(out_file2, 'w') as f:
         json.dump(out, f, indent = 4)

docker/Dockerfile.preprocessing-0.9.8.1

@@ -1,5 +1,6 @@
 FROM ubuntu:focal
 
+
 LABEL maintainer="[email protected]" \
 about.summary="container for the preprocessing workflow"
 

modules/decontaminationModules.nf

@@ -34,7 +34,7 @@ process identifyBacterialContaminants {
     report_json = "${sample_name}_report.json"
 
     """
-    identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${refseq} ${params.species} ${params.unmix_myco} ${resources} null ${params.permissive}
+    identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${refseq} ${params.species} ${params.unmix_myco} ${resources} null ${params.permissive} ${pass}
 
     contam_to_remove=\$(jq -r '.summary_questions.are_there_contaminants' ${sample_name}_species_in_sample.json)
     acceptable_species=\$(jq -r '.summary_questions.is_the_top_species_appropriate' ${sample_name}_species_in_sample.json)
@@ -340,40 +340,40 @@ process summarise {
     tuple val(sample_name), path("${sample_name}_species_in_sample.json"), stdout, emit: summary_json
     stdout emit: do_we_break
     path "${sample_name}_err.json", emit: summary_log optional true
-    path "${sample_name}_report.json", emit: summary_report optional true
+    path "${sample_name}_pass_${pass}_report.json", emit: summary_report optional true
     val(pass), emit: pass_number
 
     script:
     error_log = "${sample_name}_err.json"
-    report_json = "${sample_name}_report.json"
-
+    report_json = "${sample_name}_pass_${pass}_report.json"
+    species_in_sample = "${sample_name}_species_in_sample_pass_${pass}.json"
     """
-    identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${refseq} ${params.species} ${params.unmix_myco} ${resources} ${prev_species_json} ${params.permissive}
+    identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${refseq} ${params.species} ${params.unmix_myco} ${resources} ${prev_species_json} ${params.permissive} ${pass}
     
 
-    contam_to_remove=\$(jq -r '.summary_questions.are_there_contaminants' ${sample_name}_species_in_sample.json)
-    acceptable_species=\$(jq -r '.summary_questions.is_the_top_species_appropriate' ${sample_name}_species_in_sample.json)
-    top_hit=\$(jq -r '.top_hit.name' ${sample_name}_species_in_sample.json)
+    contam_to_remove=\$(jq -r '.summary_questions.are_there_contaminants' ${species_in_sample})
+    acceptable_species=\$(jq -r '.summary_questions.is_the_top_species_appropriate' ${species_in_sample})
+    top_hit=\$(jq -r '.top_hit.name' ${species_in_sample})
 
     if [ \$contam_to_remove == 'yes' ]; then
         if [ "${params.permissive}" == "no" ]; then
             printf "${sample_name}"
-            echo '{"error":"sample remains contaminated, even after attempting to resolve this"}' | jq '.' > ${error_log} && jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${sample_name}_species_in_sample.json > ${report_json}
+            echo '{"error":"sample remains contaminated, even after attempting to resolve this"}' | jq '.' > ${error_log} && jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${species_in_sample} > ${report_json}
         else
             if [ "${pass}" == 2 ]; then
                  printf "NOW_ALIGN_TO_REF_${sample_name}"
             else
                  printf "${sample_name}"
             fi
-            echo '{"warning":"sample remains contaminated, even after attempting to resolve this"}' | jq '.' > ${error_log} && jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${sample_name}_species_in_sample.json > ${report_json}
+            echo '{"warning":"sample remains contaminated, even after attempting to resolve this"}' | jq '.' > ${error_log} && jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${species_in_sample} > ${report_json}
         fi
     fi
 
     if [ \$contam_to_remove == 'no' ] && [ \$acceptable_species == 'yes' ]; then 
         printf "NOW_ALIGN_TO_REF_${sample_name}"
     elif [ \$contam_to_remove == 'no' ] && [ \$acceptable_species == 'no' ]; then
         jq -n --arg key "\$top_hit" '{"error": ("top hit " + \$key + " does not have a reference genome. Sample will not proceed beyond preprocessing workflow.")}' > ${error_log} && \
-        jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${sample_name}_species_in_sample.json > ${report_json}
+        jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${species_in_sample} > ${report_json}
         printf "DO_NOT_PROCEED_${sample_name}"
     fi
     """

modules/preprocessingModules.nf

@@ -374,7 +374,8 @@ process afanc {
         cp ${sample_name}/${sample_name}.json ${sample_name}_afanc_original.json
 	reformat_afanc_json.py ${sample_name}/${sample_name}.json
 
-	identify_tophit_and_contaminants2.py ${afanc_report} ${kraken_json} $refseq_path ${params.species} ${params.unmix_myco} $resource_dir null ${params.permissive}
+	identify_tophit_and_contaminants2.py ${afanc_report} ${kraken_json} $refseq_path ${params.species} ${params.unmix_myco} $resource_dir null ${params.permissive} ${pass}
+        mv "${sample_name}"_species_in_sample_pass_0.json "${sample_name}"_species_in_sample.json 
 
 	echo '{"error":"Kraken's top family hit either wasn't Mycobacteriaceae, or there were < 100k Mycobacteriaceae reads. Sample will not proceed further than afanc."}' | jq '.' > ${error_log} && printf "no" && jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${sample_name}_species_in_sample.json > ${report_json}